If Merck & Co.’s $4 billion bet on the hepatitis C drug being developed by Cambridge biotech firm Idenix Pharmaceuticals pays off, it will provide Merck with a slice of an estimated $50 billion market over the next decade.

But the way one analyst sees it, the fact that Gilead Sciences — the current king in that disease space — didn’t pony up for Idenix raises questions as to the drug’s eventual viability.

The fact that Merck is willing to pay more than triple the market value for the 84-employee biotech, which has not progressed beyond Phase 1 clinical trials, has a lot to do with the success of Gilead’s hepatitis C drug, Sovaldi. According to Seamus Levine-Wilkinson, an analyst at Boston-based healthcare research organization Decision Resources Group, both are the same type of drug, a so-called a nucleotide polymerase inhibitors, or “nuke.” The advantage of this type of drug is it neutralizes the virus in a way that can’t be overcome by a mutation, and treats all six genotypes. It’s also pill-based, therefore easy to take, and doesn’t rely on interferons, a type of drug known to cause flu-like symptoms in many patients.

“Nukes” are different from the drug in late-stage development by Watertown-based Enanta Pharmaceuticals and partner AbbVie, which is pill-based and doesn't use interferons, but only treats some of the genotypes and requires several other drugs to be used in combination. That increases the chances of interactions with other drugs the patients may also be taking, lowering the patient population even further, said Levine-Wilkinson.

A few other companies have a “nuke” in development, said Levine-Wilkinson, including Roche and Achillion Pharmaceuticals. But the fact is that Gilead, with the first such drug to reach market, is likely to rule the disease space for some time to come. Levine-Wilkinson says that surveys have shown that almost all physicians say if cost wasn’t a factor, they would prescribe Sovaldi to almost all their patients with the disease. (Cost remains a major factor, however: At $84,000 for a course of treatment, Gilead attracted negative attention from Congress in February, spooking investors enough to spur a two-month selloff in the sector).

The size of the market itself is tough top gauge, since many people with the virus go undiagnosed for years, and many who are diagnosed forgo treatment because of the side effects of interferons. But pretty much everyone agrees the population is huge, and at current pricing, it’s believed to be worth $50 billion over the next 10 years. Sovaldi is expected to top $10 billion in sales in 2014, its first full year of sales.

Considered from that point of view, said Levine-Wilkinson, Merck’s decision to pay $4 billion for Idenix may be justified. “Merck is making the calculation that they’re going to get more than 10 percent of the market,” he said, thereby paying for the acquisition and taking a profit. Idenix drug, if successful, has the potential to be more effective than Sovaldi, and to take just four weeks of treatment — half to a third of the time of Sovaldi, even with another drug Gilead has planned to pair with it.

In fact, compared to Gilead’s $10.8 billion acquisition of Pharmasset in 2011 (an 89 percent premium to the company’s value at the time) in order to get the drug that became Sovaldi, Merck’s $4 billion for Idenix could be seen as a downright steal. “If it works, it’s going to look like Merck made the same play as Gilead, albeit a few years later and at a cheaper price,” said Levine-Wilkinson.

Of course, it all depends on whether the drug makes it over the regulatory hurdles needed for approval in the next two years. While Levine-Wilkinson says the data so far indicates Idenix’s drug to be effective in reducing the amount of virus in the body, all eyes will be on the drug's safety. That, he says, is very much an open question.

“If you look at the history of nucleotide drugs, the conservative assumption is that they won’t be approved,” he said. And he says he’s not sure why, given the potential upside of Idenix, Gilead itself didn’t make the acquisition. It’s reasonable to assume Gilead poured over the data from the drug. Could they have seen something that made them decide it was too big a risk?

“You have to assume Gilead was invited to bid, and they declined for whatever reason,” he said. “Gilead’s printing money with (Sovaldi). Why didn’t they buy Idenix? That’s the biggest question that no one’s talking about.”